Hello, I hope the following information helps you.
To stop the alarm sounding if you open the door manually you need to unlock the driver's door with the key then within ten seconds of opening the door start the engine, if you don't do this within 10 seconds the alarm goes off.
Once the alarm sounds the only way to turn it off is with the remote fob or wait for it to stop after 30 seconds but it will sound again if anything is done to trigger it again.
Try fitting a new battery to the key fob once you've unlocked the car and started it to disarm the alarm, turn the ignition off then proceed as follows.NOTE: A maximum of eight keyless entry remote transmitters can be programmed to the Central Junction Box (CJB). Programming must be done at the same time for all the transmitters.NOTE: To enter programming mode, first make sure that the vehicle battery is fully charged and the anti-theft system is not armed or triggered (if equipped).
NOTE: Make sure the turn signal indicators are in the OFF position.
Fasten the safety belts and close all doors to make sure conflicting chimes do not sound during programming.
NOTE: The ignition must be turned to position II exactly four times during remote transmitter programming.
Turn the ignition switch from position I to position II four times exactly within six seconds.Turn the ignition switch to position 0.
An audible chime will be heard (only in vehicles built before 2008 model year) to indicate that it is now possible to programme the keys for ten seconds.
Press and hold one of the buttons on the remote transmitter until a chime sounds. This indicates a new transmitter code has been successfully received.
To program additional transmitters, carry out the previous step above (press and hold a button)
I hope this helps, let me know if I can assist further and I'll reply as soon as I can.